A simple, robust, cost‐effective, and low‐input ChIP‐seq method for profiling histone modifications and Pol II in plants

Summary Chromatin immunoprecipitation and sequencing (vs ChIP‐seq) is an essential tool for epigenetic and molecular genetic studies. Although being routinely used, ChIP‐seq is expensive, requires grams of plant materials, and is challenging for samples that enrich fatty acids such as seeds. Here, we developed an Ultrasensitive Plant ChIP‐seq (UP‐ChIP) method based on native ChIP‐seq combined with Tn5 tagmentation‐based library construction strategy. UP‐ChIP is generally applicable for profiling both histone modification and Pol II in a wide range of plant samples, such as a single Arabidopsis seedling, a few Arabidopsis seeds, and sorted nuclei. Compared with conventional ChIP‐seq, UP‐ChIP is much less labor intensive and only consumes 1 μg of antibody and 10 μl of Protein‐A/G conjugated beads for each IP and can work effectively with the amount of starting material down to a few milligrams. By performing UP‐ChIP in various conditions and genotypes, we showed that UP‐ChIP is highly reliable, sensitive, and quantitative for studying histone modifications. Detailed UP‐ChIP protocol is provided. We recommend UP‐ChIP as an alternative to traditional ChIP‐seq for profiling histone modifications and Pol II, offering the advantages of reduced labor intensity, decreased costs, and low‐sample input.